def setUp(self):
super(EntryResourceTest, self).setUp()
self.serializer = Serializer()
self.api_client = TestApiClient(self.serializer)
self.apiPath = "/api/" + Api.api.api_name
class EntryResourceTest(ResourceTestCase):
# Use ``fixtures`` & ``urls`` as normal. See Django's ``TestCase``
# documentation for the gory details.
fixtures = ['test_entries.json']
#-----------------------------------------------------------------------------------------------------------------------
def setUp(self):
super(EntryResourceTest, self).setUp()
self.serializer = Serializer()
self.api_client = TestApiClient(self.serializer)
self.apiPath = "/api/" + Api.api.api_name
#-----------------------------------------------------------------------------------------------------------------------
def test_get_list_json(self):
for item in Api.api._registry.items():
name = item[0]
resource = item[1]
if 'get' in resource._meta.list_allowed_methods:
url = self.apiPath + '/' + name + '/'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
#-----------------------------------------------------------------------------------------------------------------------
def test_get_schema_json(self):
for item in Api.api._registry.items():
name = item[0]
resource = item[1]
if 'get' in resource._meta.list_allowed_methods:
url = self.apiPath + '/' + name + '/schema'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
#-----------------------------------------------------------------------------------------------------------------------
def test_get_detail_json(self):
for item in Api.api._registry.items():
name = item[0]
resource = item[1]
count = resource._meta.object_class.objects.count()
first_pk = None
if count > 1:
first_pk = str(resource._meta.object_class.objects.all()[0].pk)
if 'get' in resource._meta.list_allowed_methods and first_pk:
url = self.apiPath + '/' + name + '/' + first_pk
try:
resp = self.api_client.get(url, format='json')
except TemplateDoesNotExist as err:
raise Exception(url + " " + err.message)
self.assertValidJSONResponse(resp, url)
#-----------------------------------------------------------------------------------------------------------------------
def test_get_set_json(self):
for item in Api.api._registry.items():
name = item[0]
resource = item[1]
count = resource._meta.object_class.objects.count()
first_pk = None
second_pk = None
if count > 1:
first_pk = str(resource._meta.object_class.objects.all()[0].pk)
if count == 2:
second_pk = str(
resource._meta.object_class.objects.all()[1].pk)
else:
second_pk = str(
resource._meta.object_class.objects.all()[2].pk)
if 'get' in resource._meta.list_allowed_methods and second_pk:
url = self.apiPath + '/' + name + '/set/' + first_pk + ";" + second_pk + "/"
try:
resp = self.api_client.get(url, format='json')
except TemplateDoesNotExist as err:
raise Exception(url + " " + err.message)
self.assertValidJSONResponse(resp, url)
#-----------------------------------------------------------------------------------------------------------------------
def test_post(self):
self.assertHttpCreated(
self.api_client.post(self.apiPath + '/' + 'moleculedictionary' +
'/',
format='json',
data={"structure_type": "MOL"},
content_type='json')
) # TODO: post_data has to be something meaningful...
#-----------------------------------------------------------------------------------------------------------------------
def test_put_detail(self):
for item in Api.api._registry.items():
name = item[0]
resource = item[1]
count = resource._meta.object_class.objects.count()
first_pk = None
if count > 1:
first_pk = str(resource._meta.object_class.objects.all()[0].pk)
if 'put' in resource._meta.list_allowed_methods and first_pk and False:
self.assertHttpAccepted(
self.api_client.put(self.apiPath + '/' + name + '/' +
first_pk,
format='json',
data=self.new_data)
) # TODO: new_data has to be something meaningful...
#-----------------------------------------------------------------------------------------------------------------------
def test_delete_detail(self):
for item in Api.api._registry.items():
name = item[0]
resource = item[1]
count = resource._meta.object_class.objects.count()
first_pk = None
if count > 1:
first_pk = str(resource._meta.object_class.objects.all()[0].pk)
if 'delete' in resource._meta.list_allowed_methods and first_pk and False:
self.assertHttpAccepted(
self.api_client.delete(self.apiPath + '/' + name + '/' +
first_pk,
format='json'))
self.assertEqual(resource._meta.object_class.objects.count(),
count - 1)
#-----------------------------------------------------------------------------------------------------------------------
class EntryResourceTest(ResourceTestCase):
# Use ``fixtures`` & ``urls`` as normal. See Django's ``TestCase``
# documentation for the gory details.
fixtures = ['test_entries.json']
#-----------------------------------------------------------------------------------------------------------------------
def setUp(self):
super(EntryResourceTest, self).setUp()
self.serializer = Serializer()
self.api_client = TestApiClient(self.serializer)
self.apiPath = "/api/" + Api.api.api_name
#-----------------------------------------------------------------------------------------------------------------------
def test_get_list_json(self):
for item in Api.api._registry.items():
name = item[0]
resource = item[1]
if 'get' in resource._meta.list_allowed_methods:
url = self.apiPath + '/' + name + '/'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
#-----------------------------------------------------------------------------------------------------------------------
def test_get_schema_json(self):
for item in Api.api._registry.items():
name = item[0]
resource = item[1]
if 'get' in resource._meta.list_allowed_methods:
url = self.apiPath + '/' + name + '/schema'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
#-----------------------------------------------------------------------------------------------------------------------
def test_get_detail_json(self):
for item in Api.api._registry.items():
name = item[0]
resource = item[1]
count = resource._meta.object_class.objects.count()
first_pk = None
if count > 1:
first_pk = str(resource._meta.object_class.objects.all()[0].pk)
if 'get' in resource._meta.list_allowed_methods and first_pk:
url = self.apiPath + '/' + name + '/' + first_pk
try:
resp = self.api_client.get(url, format='json')
except TemplateDoesNotExist as err:
raise Exception(url + " " + err.message)
self.assertValidJSONResponse(resp, url)
#-----------------------------------------------------------------------------------------------------------------------
def test_get_set_json(self):
for item in Api.api._registry.items():
name = item[0]
resource = item[1]
count = resource._meta.object_class.objects.count()
first_pk = None
second_pk = None
if count > 1:
first_pk = str(resource._meta.object_class.objects.all()[0].pk)
if count == 2:
second_pk = str(resource._meta.object_class.objects.all()[1].pk)
else:
second_pk = str(resource._meta.object_class.objects.all()[2].pk)
if 'get' in resource._meta.list_allowed_methods and second_pk:
url = self.apiPath + '/' + name + '/set/' + first_pk + ";" + second_pk + "/"
try:
resp = self.api_client.get(url, format='json')
except TemplateDoesNotExist as err:
raise Exception(url + " " + err.message)
self.assertValidJSONResponse(resp, url)
#-----------------------------------------------------------------------------------------------------------------------
def test_post(self):
self.assertHttpCreated(self.api_client.post(self.apiPath + '/' + 'moleculedictionary' + '/', format='json', data={"structure_type": "MOL"}, content_type='json')) # TODO: post_data has to be something meaningful...
#-----------------------------------------------------------------------------------------------------------------------
def test_put_detail(self):
for item in Api.api._registry.items():
name = item[0]
resource = item[1]
count = resource._meta.object_class.objects.count()
first_pk = None
if count > 1:
first_pk = str(resource._meta.object_class.objects.all()[0].pk)
if 'put' in resource._meta.list_allowed_methods and first_pk and False:
self.assertHttpAccepted(self.api_client.put(self.apiPath + '/' + name + '/' + first_pk, format='json', data=self.new_data)) # TODO: new_data has to be something meaningful...
#-----------------------------------------------------------------------------------------------------------------------
def test_delete_detail(self):
for item in Api.api._registry.items():
name = item[0]
resource = item[1]
count = resource._meta.object_class.objects.count()
first_pk = None
if count > 1:
first_pk = str(resource._meta.object_class.objects.all()[0].pk)
if 'delete' in resource._meta.list_allowed_methods and first_pk and False:
self.assertHttpAccepted(self.api_client.delete(self.apiPath + '/' + name + '/' + first_pk, format='json'))
self.assertEqual(resource._meta.object_class.objects.count(), count - 1)
#-----------------------------------------------------------------------------------------------------------------------
def setUp(self):
super(EntryResourceTest, self).setUp()
self.serializer = Serializer()
self.api_client = TestApiClient(self.serializer)
self.apiPath = "/api/" + Api.api.api_name
class EntryResourceTest(ResourceTestCase):
# Use ``fixtures`` & ``urls`` as normal. See Django's ``TestCase``
# documentation for the gory details.
fixtures = ['test_entries.json']
#-----------------------------------------------------------------------------------------------------------------------
def setUp(self):
super(EntryResourceTest, self).setUp()
self.serializer = ChEMBLApiSerializer()
self.api_client = TestApiClient(self.serializer)
self.apiPath = "/chembl_webservices/" + api.api_name
#-----------------------------------------------------------------------------------------------------------------------
def deserialize(self, resp, format=None, tag=None):
form = format
if not form:
form = resp['Content-Type']
return self.serializer.deserialize(resp.content, format=form, tag=tag)
#-----------------------------------------------------------------------------------------------------------------------
def test_status(self):
url = self.apiPath + '/status/'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
self.assertEquals(self.deserialize(resp, format='application/xml', tag='service')['status'], 'UP')
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
self.assertEquals(self.deserialize(resp, format='application/json')['service']['status'], 'UP')
url = self.apiPath + '/status.json'
resp = self.api_client.get(url, format='html')
self.assertValidJSONResponse(resp, url)
self.assertEquals(self.deserialize(resp, format='application/json')['service']['status'], 'UP')
url = self.apiPath + '/status.xml'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
self.assertEquals(self.deserialize(resp, format='application/xml', tag='service')['status'], 'UP')
#-----------------------------------------------------------------------------------------------------------------------
def test_compounds(self):
url = self.apiPath + '/compounds/CHEMBL1'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
url = self.apiPath + '/compounds/CHEMBL1.json'
resp = self.api_client.get(url, format='html')
self.assertValidJSONResponse(resp, url)
url = self.apiPath + '/compounds/CHEMBL1.xml'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
url = self.apiPath + '/compounds/CHEMBL1'
resp = self.api_client.get(url, format='json')
compound = self.deserialize(resp, format='application/json')['compound']
self.assertEquals(compound['smiles'],
'COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56')
self.assertEquals(compound['chemblId'], 'CHEMBL1')
self.assertEquals(compound['medChemFriendly'], 'Yes')
self.assertEquals(compound['molecularWeight'], 544.59)
self.assertEquals(compound['molecularFormula'], 'C32H32O8')
self.assertEquals(compound['acdLogp'], 7.67)
empty = False
try:
compound['synonyms']
except KeyError:
empty = True
self.assertTrue(empty)
self.assertEquals(compound['stdInChiKey'], 'GHBOEFUAGSHXPO-XZOTUCIWSA-N')
self.assertEquals(compound['knownDrug'], 'No')
self.assertEquals(compound['passesRuleOfThree'], 'No')
self.assertEquals(compound['rotatableBonds'], 2)
empty = False
try:
compound['acdAcidicPka']
except KeyError:
empty = True
self.assertTrue(empty)
self.assertEquals(compound['alogp'], 3.63)
self.assertEquals(compound['acdLogd'], 7.67)
url = self.apiPath + '/compounds/CHEMBLX'
resp = self.api_client.get(url, format='html')
self.assertHttpBadRequest(resp)
url = self.apiPath + '/compounds/CHEMBL1642'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
url = self.apiPath + '/compounds/CHEMBL1000000000'
resp = self.api_client.get(url, format='html')
self.assertHttpNotFound(resp)
url = self.apiPath + '/compounds/CHEMBL1235452'
resp = self.api_client.get(url, format='html')
self.assertHttpNotFound(resp)
url = self.apiPath + '/compounds/stdinchikey/QFFGVLORLPOAEC-SNVBAGLBSA-N'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
compound = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(compound['chemblId'], 'CHEMBL1201760')
self.assertEquals(compound['preferredCompoundName'], 'BESIFLOXACIN')
self.assertEquals(compound['synonyms'], 'Besifloxacin')
self.assertEquals(compound['knownDrug'], 'Yes')
self.assertEquals(compound['medChemFriendly'], 'No')
self.assertEquals(compound['passesRuleOfThree'], 'No')
self.assertEquals(compound['molecularFormula'], 'C19H21ClFN3O3')
self.assertEquals(compound['smiles'], 'N[C@@H]1CCCCN(C1)c2c(F)cc3C(=O)C(=CN(C4CC4)c3c2Cl)C(=O)O')
self.assertEquals(compound['stdInChiKey'], 'QFFGVLORLPOAEC-SNVBAGLBSA-N')
self.assertEquals(compound['species'], 'ZWITTERION')
self.assertEquals(compound['numRo5Violations'], '0')
self.assertEquals(compound['rotatableBonds'], '3')
self.assertEquals(compound['molecularWeight'], '393.84')
self.assertEquals(compound['alogp'], '0.32')
self.assertEquals(compound['acdAcidicPka'], '6.41')
self.assertEquals(compound['acdBasicPka'], '10.22')
self.assertEquals(compound['acdLogp'], '3.40')
self.assertEquals(compound['acdLogd'], '0.90')
url = self.apiPath + '/compounds/stdinchikey/QFFGVLORLPOAEC-'
resp = self.api_client.get(url, format='html')
self.assertHttpBadRequest(resp)
url = self.apiPath + '/compounds/stdinchikey/QFFGVLORLPOAEK-SNVBAGLBSA-N'
resp = self.api_client.get(url, format='html')
self.assertHttpNotFound(resp)
url = self.apiPath + '/compounds/smiles/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc9cc(OC)ccc9[C@H]56'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 2)
url = self.apiPath + '/compounds/smiles/Nc1cccc2C(=O)N(C3CCC(=O)NC3=O)C(=O)c12'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 3)
url = self.apiPath + '/compounds/smiles/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 2)
compound = compounds[1]
self.assertEquals(compound['chemblId'], 'CHEMBL1')
self.assertEquals(compound['knownDrug'], 'No')
self.assertEquals(compound['medChemFriendly'], 'Yes')
self.assertEquals(compound['passesRuleOfThree'], 'No')
self.assertEquals(compound['molecularFormula'], 'C32H32O8')
self.assertEquals(compound['smiles'], 'COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56')
self.assertEquals(compound['stdInChiKey'], 'GHBOEFUAGSHXPO-XZOTUCIWSA-N')
self.assertEquals(compound['numRo5Violations'], '1')
self.assertEquals(compound['rotatableBonds'], '2')
self.assertEquals(compound['molecularWeight'], '544.59')
self.assertEquals(compound['alogp'], '3.63')
self.assertEquals(compound['acdLogp'], '7.67')
self.assertEquals(compound['acdLogd'], '7.67')
url = self.apiPath + '/compounds/smiles/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 2)
url = self.apiPath + '/compounds/smiles/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
compounds = self.deserialize(resp, format='application/json')['compounds']
self.assertEquals(len(compounds), 2)
url = self.apiPath + '/compounds/smiles/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56.xml'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 2)
url = self.apiPath + '/compounds/smiles/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56.json'
resp = self.api_client.get(url, format='html')
self.assertValidJSONResponse(resp, url)
compounds = self.deserialize(resp, format='application/json')['compounds']
self.assertEquals(len(compounds), 2)
url = self.apiPath + '/compounds/smiles/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C'
resp = self.api_client.get(url, format='html')
self.assertHttpBadRequest(resp)
url = self.apiPath + '/compounds/smiles/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC=C3C(=O)C(=O)C'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 0)
url = self.apiPath + '/compounds/smiles/xxxxx'
resp = self.api_client.get(url, format='html')
self.assertHttpBadRequest(resp)
url = self.apiPath + '/compounds/smiles.json'
resp = self.api_client.post(url, format='html',
data={'smiles':
'COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56'})
self.assertValidJSONResponse(resp, url)
compounds = self.deserialize(resp, format='application/json')['compounds']
self.assertEquals(len(compounds), 2)
compound = compounds[1]
self.assertEquals(compound['chemblId'], 'CHEMBL1')
self.assertEquals(compound['knownDrug'], 'No')
self.assertEquals(compound['medChemFriendly'], 'Yes')
self.assertEquals(compound['passesRuleOfThree'], 'No')
self.assertEquals(compound['molecularFormula'], 'C32H32O8')
self.assertEquals(compound['smiles'],
'COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56')
self.assertEquals(compound['stdInChiKey'], 'GHBOEFUAGSHXPO-XZOTUCIWSA-N')
self.assertEquals(compound['numRo5Violations'], 1)
self.assertEquals(compound['rotatableBonds'], 2)
self.assertEquals(compound['molecularWeight'], 544.59)
self.assertEquals(compound['alogp'], 3.63)
self.assertEquals(compound['acdLogp'], 7.67)
self.assertEquals(compound['acdLogd'], 7.67)
url = self.apiPath + '/compounds/smiles.xml'
resp = self.api_client.post(url, format='html',
data={'smiles':
'COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56'})
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 2)
url = self.apiPath + '/compounds/smiles'
resp = self.api_client.post(url, format='html',
data={'smiles':
'COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56'})
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 2)
url = self.apiPath + '/compounds/smiles'
resp = self.api_client.post(url, format='xml',
data={'smiles':
'COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56'})
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 2)
url = self.apiPath + '/compounds/smiles'
resp = self.api_client.post(url, format='json',
data={'smiles':
'COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56'})
self.assertValidJSONResponse(resp, url)
compounds = self.deserialize(resp, format='application/json')['compounds']
self.assertEquals(len(compounds), 2)
#-----------------------------------------------------------------------------------------------------------------------
def test_substructure(self):
url = self.apiPath + '/compounds/substructure/CCCc1nn(C)c2C(=O)NC(=Nc12)c3cc(ccc3OCC)S(=O)(=O)N4CCN(C)CC4'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 28)
url = self.apiPath + '/compounds/substructure/CCCc1nn(C)c2C(=O)NC(=Nc12)c3cc(ccc3OCC)S(=O)(=O)N4CCN(C)CC4'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
compounds = self.deserialize(resp, format='application/json')['compounds']
self.assertEquals(len(compounds), 28)
url = self.apiPath + '/compounds/substructure/CCCc1nn(C)c2C(=O)NC(=Nc12)c3cc(ccc3OCC)S(=O)(=O)N4CCN(C)CC4.xml'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 28)
url = self.apiPath + '/compounds/substructure/CCCc1nn(C)c2C(=O)NC(=Nc12)c3cc(ccc3OCC)S(=O)(=O)N4CCN(C)CC4'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 28)
url = self.apiPath + '/compounds/substructure/CCCc1nn(C)c2C(=O)NC(=Nc12)c3cc(ccc3OCC)S(=O)(=O)N4CCN(C)CC4.json'
resp = self.api_client.get(url, format='html')
self.assertValidJSONResponse(resp, url)
compounds = self.deserialize(resp, format='application/json')['compounds']
self.assertEquals(len(compounds), 28)
url = self.apiPath + '/compounds/substructure.json'
resp = self.api_client.post(url, format='html',
data={'smiles':'CCCc1nn(C)c2C(=O)NC(=Nc12)c3cc(ccc3OCC)S(=O)(=O)N4CCN(C)CC4'})
self.assertValidJSONResponse(resp, url)
compounds = self.deserialize(resp, format='application/json')['compounds']
self.assertEquals(len(compounds), 28)
url = self.apiPath + '/compounds/substructure.xml'
resp = self.api_client.post(url, format='html',
data={'smiles':'CCCc1nn(C)c2C(=O)NC(=Nc12)c3cc(ccc3OCC)S(=O)(=O)N4CCN(C)CC4'})
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 28)
url = self.apiPath + '/compounds/substructure'
resp = self.api_client.post(url, format='html',
data={'smiles':'CCCc1nn(C)c2C(=O)NC(=Nc12)c3cc(ccc3OCC)S(=O)(=O)N4CCN(C)CC4'})
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 28)
url = self.apiPath + '/compounds/substructure'
resp = self.api_client.post(url, format='json',
data={'smiles':'CCCc1nn(C)c2C(=O)NC(=Nc12)c3cc(ccc3OCC)S(=O)(=O)N4CCN(C)CC4'})
self.assertValidJSONResponse(resp, url)
compounds = self.deserialize(resp, format='application/json')['compounds']
self.assertEquals(len(compounds), 28)
url = self.apiPath + '/compounds/substructure/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 0)
#-----------------------------------------------------------------------------------------------------------------------
def test_similarity(self):
url = self.apiPath + '/compounds/similarity/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56/95'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 9)
url = self.apiPath + '/compounds/similarity/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56/95'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
compounds = self.deserialize(resp, format='application/json')['compounds']
for compound in compounds:
self.assertTrue(95 <= compound['similarity'] <= 100)
self.assertEquals(len(compounds), 9)
url = self.apiPath + '/compounds/similarity/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56/95'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 9)
url = self.apiPath + '/compounds/similarity/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56/95.json'
resp = self.api_client.get(url, format='html')
self.assertValidJSONResponse(resp, url)
compounds = self.deserialize(resp, format='application/json')['compounds']
self.assertEquals(len(compounds), 9)
url = self.apiPath + '/compounds/similarity/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56/95.xml'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 9)
url = self.apiPath + '/compounds/similarity.json'
resp = self.api_client.post(url, format='html', data={'smiles':'COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56', 'simscore': 95})
self.assertValidJSONResponse(resp, url)
compounds = self.deserialize(resp, format='application/json')['compounds']
self.assertEquals(len(compounds), 9)
url = self.apiPath + '/compounds/similarity.xml'
resp = self.api_client.post(url, format='html', data={'smiles':'COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56', 'simscore': 95})
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 9)
url = self.apiPath + '/compounds/similarity'
resp = self.api_client.post(url, format='html', data={'smiles':'COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56', 'simscore': 95})
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 9)
url = self.apiPath + '/compounds/similarity'
resp = self.api_client.post(url, format='json', data={'smiles':'COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56', 'simscore': 95})
self.assertValidJSONResponse(resp, url)
compounds = self.deserialize(resp, format='application/json')['compounds']
self.assertEquals(len(compounds), 9)
url = self.apiPath + '/compounds/similarity'
resp = self.api_client.post(url, format='json', content_type='json', data={'smiles':'COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56', 'simscore': 95})
self.assertValidJSONResponse(resp, url)
compounds = self.deserialize(resp, format='application/json')['compounds']
self.assertEquals(len(compounds), 9)
url = self.apiPath + '/compounds/similarity/CCc1nn(C)c2C(=O)NC(=Nc12)c3cc(ccc3OCC)S(=O)(=O)N4CCN(C)CC4/100'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 0)
url = self.apiPath + '/compounds/similarity/CCc1nn(C)c2C(=O)NC(=Nc12)c3cc(/100'
resp = self.api_client.get(url, format='html')
self.assertHttpBadRequest(resp)
url = self.apiPath + '/compounds/similarity/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56/69'
resp = self.api_client.get(url, format='html')
self.assertHttpBadRequest(resp)
url = self.apiPath + '/compounds/similarity/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56/101'
resp = self.api_client.get(url, format='html')
self.assertHttpBadRequest(resp)
url = self.apiPath + '/compounds/similarity/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56/bla'
resp = self.api_client.get(url, format='html')
self.assertHttpNotFound(resp)
#-----------------------------------------------------------------------------------------------------------------------
def test_image(self):
url = self.apiPath + '/compounds/CHEMBL192/image'
resp = self.api_client.get(url, format='html')
self.assertHttpOK(resp)
self.assertEquals(resp['Content-Type'], 'image/png')
url = self.apiPath + '/compounds/CHEMBL192/image?dimensions=200'
resp = self.api_client.get(url, format='html')
self.assertHttpOK(resp)
self.assertEquals(resp['Content-Type'], 'image/png')
url = self.apiPath + '/compounds/CHEMBL192/image?dimensions=0'
resp = self.api_client.get(url, format='html')
self.assertHttpBadRequest(resp)
url = self.apiPath + '/compounds/CHEMBL192/image?dimensions=550'
resp = self.api_client.get(url, format='html')
self.assertHttpBadRequest(resp)
url = self.apiPath + '/compounds/CHEMBLX/image'
resp = self.api_client.get(url, format='html')
self.assertHttpBadRequest(resp)
url = self.apiPath + '/compounds/CHEMBL10000000000/image'
resp = self.api_client.get(url, format='html')
self.assertHttpNotFound(resp)
#-----------------------------------------------------------------------------------------------------------------------
def test_compound_bioactivities(self):
url = self.apiPath + '/compounds/CHEMBL2/bioactivities'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
bioactivities = self.deserialize(resp, format='application/xml', tag='bioactivity')
self.assertTrue(len(bioactivities) > 900)
url = self.apiPath + '/compounds/CHEMBL2/bioactivities'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
bioactivities = self.deserialize(resp, format='application/xml', tag='bioactivity')
self.assertTrue(len(bioactivities) > 900)
url = self.apiPath + '/compounds/CHEMBL2/bioactivities.xml'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
bioactivities = self.deserialize(resp, format='application/xml', tag='bioactivity')
self.assertTrue(len(bioactivities) > 900)
url = self.apiPath + '/compounds/CHEMBL2/bioactivities.json'
resp = self.api_client.get(url, format='html')
self.assertValidJSONResponse(resp, url)
bioactivities = self.deserialize(resp, format='application/json')['bioactivities']
self.assertTrue(len(bioactivities) > 900)
url = self.apiPath + '/compounds/CHEMBL2/bioactivities'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
bioactivities = self.deserialize(resp, format='application/json')['bioactivities']
self.assertTrue(len(bioactivities) > 900)
url = self.apiPath + '/compounds/CHEMBL101/bioactivities.xml'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
url = self.apiPath + '/compounds/CHEMBLX/bioactivities'
resp = self.api_client.get(url, format='json')
self.assertHttpBadRequest(resp)
url = self.apiPath + '/compounds/CHEMBL10000000000/bioactivities'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
bioactivities = self.deserialize(resp, format='application/json')['bioactivities']
self.assertEquals(len(bioactivities), 0)
#-----------------------------------------------------------------------------------------------------------------------
def test_targets(self):
url = self.apiPath + '/targets/CHEMBL2477'
resp = self.api_client.get(url, format='xml')
self.assertHttpNotFound(resp)
url = self.apiPath + '/targets/CHEMBL2478'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
url = self.apiPath + '/targets/CHEMBL2478'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
url = self.apiPath + '/targets/CHEMBL2478.xml'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
url = self.apiPath + '/targets/CHEMBL2478.json'
resp = self.api_client.get(url, format='html')
self.assertValidJSONResponse(resp, url)
url = self.apiPath + '/targets/CHEMBL2478'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
url = self.apiPath + '/targets/CHEMBL2478'
resp = self.api_client.get(url, format='json')
target = self.deserialize(resp, format='application/json')['target']
self.assertEquals(target['chemblId'], 'CHEMBL2478')
self.assertEquals(target['targetType'], 'SINGLE PROTEIN')
self.assertEquals(target['preferredName'], 'Salivary alpha-amylase')
self.assertEquals(target['proteinAccession'], 'P04745')
self.assertEquals(set(target['synonyms'].split(DEFAULT_TARGET_SEPARATOR)), set(['Salivary alpha-amylase',
'andAMY1','Alpha-amylase 1','AMY1','4-alpha-D-glucan glucanohydrolase 1','AMY1C','1', '3.2.1.1',]))
self.assertEquals(target['organism'], 'H**o sapiens')
self.assertEquals(target['description'], 'Salivary alpha-amylase')
self.assertEquals(target['geneNames'], 'Unspecified')
self.assertEquals(target['compoundCount'], 29)
self.assertEquals(target['bioactivityCount'], 52)
url = self.apiPath + '/targets/CHEMBLX'
resp = self.api_client.get(url, format='html')
self.assertHttpBadRequest(resp)
url = self.apiPath + '/targets/CHEMBL1000000000'
resp = self.api_client.get(url, format='html')
self.assertHttpNotFound(resp)
#-----------------------------------------------------------------------------------------------------------------------
def test_targets_uniprot(self):
url = self.apiPath + '/targets/uniprot/Q13936'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
url = self.apiPath + '/targets/uniprot/Q13936'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
url = self.apiPath + '/targets/uniprot/Q13936.xml'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
url = self.apiPath + '/targets/uniprot/Q13936.json'
resp = self.api_client.get(url, format='html')
self.assertValidJSONResponse(resp, url)
url = self.apiPath + '/targets/uniprot/Q13936'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
url = self.apiPath + '/targets/uniprot_all/Q13936'
resp = self.api_client.get(url, format='xml')
targets = self.deserialize(resp, format='application/xml', tag='target')
self.assertEquals(len(targets), 3)
target = targets[0]
self.assertEquals(target['chemblId'], 'CHEMBL1940')
self.assertEquals(target['targetType'], 'SINGLE PROTEIN')
self.assertEquals(target['preferredName'], 'Voltage-gated L-type calcium channel alpha-1C subunit')
self.assertEquals(target['proteinAccession'], 'Q13936')
self.assertEquals(set(target['synonyms'].split(DEFAULT_TARGET_SEPARATOR)), set(['CACH2 ','CACN2',
'Voltage-gated calcium channel subunit alpha Cav1.2','CACNA1C','Calcium channel',' L type',
' alpha-1 polypeptide',' isoform 1',' cardiac muscle','CCHL1A1','CACNL1A1',
'Voltage-dependent L-type calcium channel subunit alpha-1C']))
self.assertEquals(target['organism'], 'H**o sapiens')
self.assertEquals(target['description'], 'Voltage-gated L-type calcium channel alpha-1C subunit')
self.assertEquals(target['geneNames'], 'Unspecified')
self.assertTrue(target['compoundCount'] > '170')
self.assertTrue(target['bioactivityCount'] > '200')
url = self.apiPath + '/targets/uniprot/Q13936'
resp = self.api_client.get(url, format='xml')
target = self.deserialize(resp, format='application/xml', tag='target')
self.assertEquals(target['chemblId'], 'CHEMBL1940')
self.assertEquals(target['targetType'], 'SINGLE PROTEIN')
self.assertEquals(target['preferredName'], 'Voltage-gated L-type calcium channel alpha-1C subunit')
self.assertEquals(target['proteinAccession'], 'Q13936')
self.assertEquals(set(target['synonyms'].split(DEFAULT_TARGET_SEPARATOR)), set(['CACH2 ','CACN2',
'Voltage-gated calcium channel subunit alpha Cav1.2','CACNA1C','Calcium channel',' L type',
' alpha-1 polypeptide',' isoform 1',' cardiac muscle','CCHL1A1','CACNL1A1',
'Voltage-dependent L-type calcium channel subunit alpha-1C']))
self.assertEquals(target['organism'], 'H**o sapiens')
self.assertEquals(target['description'], 'Voltage-gated L-type calcium channel alpha-1C subunit')
self.assertEquals(target['geneNames'], 'Unspecified')
self.assertTrue(target['compoundCount'] > '170')
self.assertTrue(target['bioactivityCount'] > '230')
url = self.apiPath + '/targets/uniprot/Q139367'
resp = self.api_client.get(url, format='html')
self.assertHttpBadRequest(resp)
url = self.apiPath + '/targets/uniprot/Q03936'
resp = self.api_client.get(url, format='html')
self.assertHttpNotFound(resp)
#-----------------------------------------------------------------------------------------------------------------------
def test_targets_refseq(self):
'''
refseq shuld be removed
'''
url = self.apiPath + '/targets/refseq/P_001128722'
resp = self.api_client.get(url, format='html')
self.assertHttpBadRequest(resp)
url = self.apiPath + '/targets/refseq/NP_001128722'
resp = self.api_client.get(url, format='html')
self.assertHttpNotFound(resp)
#-----------------------------------------------------------------------------------------------------------------------
def test_target_bioactivities(self):
url = self.apiPath + '/targets/CHEMBL241/bioactivities'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
bioactivities = self.deserialize(resp, format='application/xml', tag='bioactivity')
self.assertTrue(len(bioactivities) > 600)
url = self.apiPath + '/targets/CHEMBL241/bioactivities'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
bioactivities = self.deserialize(resp, format='application/xml', tag='bioactivity')
self.assertTrue(len(bioactivities) > 600)
url = self.apiPath + '/targets/CHEMBL241/bioactivities.xml'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
bioactivities = self.deserialize(resp, format='application/xml', tag='bioactivity')
self.assertTrue(len(bioactivities) > 600)
url = self.apiPath + '/targets/CHEMBL241/bioactivities.json'
resp = self.api_client.get(url, format='html')
self.assertValidJSONResponse(resp, url)
bioactivities = self.deserialize(resp, format='application/json')['bioactivities']
self.assertTrue(len(bioactivities) > 600)
url = self.apiPath + '/targets/CHEMBL241/bioactivities'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
bioactivities = self.deserialize(resp, format='application/json')['bioactivities']
self.assertTrue(len(bioactivities) > 600)
url = self.apiPath + '/targets/CHEMBLX/bioactivities'
resp = self.api_client.get(url, format='json')
self.assertHttpBadRequest(resp)
url = self.apiPath + '/targets/CHEMBL10000000000/bioactivities'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
bioactivities = self.deserialize(resp, format='application/json')['bioactivities']
self.assertEquals(len(bioactivities), 0)
#-----------------------------------------------------------------------------------------------------------------------
def test_assays(self):
url = self.apiPath + '/assays/CHEMBL1217643'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
url = self.apiPath + '/assays/CHEMBL1217643'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
url = self.apiPath + '/assays/CHEMBL1217643.xml'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
url = self.apiPath + '/assays/CHEMBL1217643.json'
resp = self.api_client.get(url, format='html')
self.assertValidJSONResponse(resp, url)
url = self.apiPath + '/assays/CHEMBL1217643'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
url = self.apiPath + '/assays/CHEMBL1217643'
resp = self.api_client.get(url, format='json')
assay = self.deserialize(resp, format='application/json')['assay']
self.assertEquals(assay['chemblId'], 'CHEMBL1217643')
self.assertEquals(assay['assayType'], 'B')
self.assertEquals(assay['journal'], 'Bioorg. Med. Chem. Lett.')
self.assertEquals(assay['assayOrganism'], 'H**o sapiens')
self.assertEquals(assay['assayStrain'], 'Unspecified')
self.assertEquals(assay['assayDescription'], 'Inhibition of human hERG')
self.assertEquals(assay['numBioactivities'], 1)
url = self.apiPath + '/assays/CHEMBLX'
resp = self.api_client.get(url, format='html')
self.assertHttpBadRequest(resp)
url = self.apiPath + '/assays/CHEMBL1000000000'
resp = self.api_client.get(url, format='html')
self.assertHttpNotFound(resp)
#-----------------------------------------------------------------------------------------------------------------------
def test_assay_bioactivities(self):
url = self.apiPath + '/assays/CHEMBL1217643/bioactivities'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
bioactivities = self.deserialize(resp, format='application/xml', tag='bioactivity')
self.assertEquals(len(bioactivities), 1)
bioactivity = bioactivities[0]
self.assertEquals(bioactivity['parent__cmpd__chemblid'], 'CHEMBL1214402')
self.assertEquals(bioactivity['ingredient__cmpd__chemblid'], 'CHEMBL1214402')
self.assertEquals(bioactivity['target__chemblid'], 'CHEMBL240')
self.assertEquals(bioactivity['target__confidence'], '9')
self.assertEquals(bioactivity['target__name'], 'HERG')
self.assertEquals(bioactivity['reference'], 'Bioorg. Med. Chem. Lett., (2010) 20:15:4359')
self.assertEquals(bioactivity['name__in__reference'], '26')
self.assertEquals(bioactivity['organism'], 'H**o sapiens')
self.assertEquals(bioactivity['bioactivity__type'], 'IC50')
self.assertEquals(bioactivity['activity__comment'], 'Unspecified')
self.assertEquals(bioactivity['operator'], '=')
self.assertEquals(bioactivity['units'], 'nM')
self.assertEquals(bioactivity['assay__chemblid'], 'CHEMBL1217643')
self.assertEquals(bioactivity['assay__type'], 'B')
self.assertEquals(bioactivity['assay__description'], 'Inhibition of human hERG')
self.assertEquals(bioactivity['value'], '5900')
url = self.apiPath + '/assays/CHEMBL1217643/bioactivities'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
bioactivities = self.deserialize(resp, format='application/xml', tag='bioactivity')
self.assertEquals(len(bioactivities), 1)
url = self.apiPath + '/assays/CHEMBL1217643/bioactivities.xml'
resp = self.api_client.get(url, format='html')
self.assertValidXMLResponse(resp)
bioactivities = self.deserialize(resp, format='application/xml', tag='bioactivity')
self.assertEquals(len(bioactivities), 1)
url = self.apiPath + '/assays/CHEMBL1217643/bioactivities.json'
resp = self.api_client.get(url, format='html')
self.assertValidJSONResponse(resp, url)
bioactivities = self.deserialize(resp, format='application/json')['bioactivities']
self.assertEquals(len(bioactivities), 1)
url = self.apiPath + '/assays/CHEMBL1217643/bioactivities'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
bioactivities = self.deserialize(resp, format='application/json')['bioactivities']
self.assertEquals(len(bioactivities), 1)
url = self.apiPath + '/assays/CHEMBLX/bioactivities'
resp = self.api_client.get(url, format='json')
self.assertHttpBadRequest(resp)
url = self.apiPath + '/assays/CHEMBL10000000000/bioactivities'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
bioactivities = self.deserialize(resp, format='application/json')['bioactivities']
self.assertEquals(len(bioactivities), 0)
#-----------------------------------------------------------------------------------------------------------------------
def test_explode(self):
url = self.apiPath + '/compounds.xml?chemblid=CHEMBL104&explode_synonyms=true'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
url = self.apiPath + '/compounds.xml?chemblid=CHEMBL104'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
compound = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(set(compound['synonyms'].split(DEFAULT_COMPOUND_SEPARATOR)),
set(['Gynix','GNF-Pf-3499',
'Gyne-Lotrimin 3 Combination Pack','Canesten','Gyne-lotrimin','BAY-5097',
'Gyne-Lotrimin 3','Gyne-Lotrimin Combination Pack','Mycelex-7 Combination Pack',
'Mycelex-G','Clotrimazole',
'Gyne-Lotrimin','Mycelex-7','Trivagizole 3','Mycelex','SID90340692', 'SID85230973',
]))
url = self.apiPath + '/compounds.xml?smiles=CN1CCN(Cc2ccc(cc2)C(=O)Nc3ccc(C)c(Nc4nccc(n4)c5cccnc5)c3)CC1&explode_synonyms=true'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
compounds = self.deserialize(resp, format='application/xml', tag='compound')
self.assertEquals(len(compounds), 2)
url = self.apiPath + '/compounds.xml?stdinchikey=LFQSCWFLJHTTHZ-UHFFFAOYSA-N&explode_synonyms=true'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
#-----------------------------------------------------------------------------------------------------------------------
def test_compound_drug_mechinsims(self):
url = self.apiPath + '/compounds/CHEMBL1200550/drugMechanism'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
drug_mechanisms = self.deserialize(resp, format='application/xml', tag='drugMechanism')
self.assertEquals(len(drug_mechanisms), 1)
mechanism = drug_mechanisms[0]
self.assertEquals(mechanism['chemblId'], 'CHEMBL231')
self.assertEquals(mechanism['name'], 'Histamine H1 receptor')
self.assertEquals(mechanism['mechanismOfAction'], 'Histamine H1 receptor antagonist')
url = self.apiPath + '/compounds/CHEMBL1642/drugMechanism.json'
resp = self.api_client.get(url, format='html')
self.assertValidJSONResponse(resp, url)
drug_mechanisms = self.deserialize(resp, format='application/json')['drugMechanisms']
self.assertEquals(len(drug_mechanisms), 3)
url = self.apiPath + '/compounds/CHEMBL941/drugMechanism'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
drug_mechanisms = self.deserialize(resp, format='application/json')['drugMechanisms']
self.assertEquals(len(drug_mechanisms), 0)
url = self.apiPath + '/compounds/CHEMBLX/drugMechanism'
resp = self.api_client.get(url, format='json')
self.assertHttpBadRequest(resp)
url = self.apiPath + '/compounds/CHEMBL10000000000/drugMechanism'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
drug_mechanisms = self.deserialize(resp, format='application/json')['drugMechanisms']
self.assertEquals(len(drug_mechanisms), 0)
#-----------------------------------------------------------------------------------------------------------------------
def test_target_approved_drugs(self):
url = self.apiPath + '/targets/CHEMBL1824/approvedDrug.xml'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
approved_drugs = self.deserialize(resp, format='application/xml', tag='approvedDrug')
self.assertTrue(len(approved_drugs) >= 4)
drug = approved_drugs[0]
self.assertEquals(drug['chemblId'], 'CHEMBL1201585')
self.assertEquals(drug['name'], 'TRASTUZUMAB')
self.assertEquals(drug['mechanismOfAction'], 'Receptor protein-tyrosine kinase erbB-2 inhibitor')
url = self.apiPath + '/targets/CHEMBLX/approvedDrug'
resp = self.api_client.get(url, format='json')
self.assertHttpBadRequest(resp)
url = self.apiPath + '/targets/CHEMBL10000000000/approvedDrug'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
drug_mechanisms = self.deserialize(resp, format='application/json')['approvedDrugs']
self.assertEquals(len(drug_mechanisms), 0)
#-----------------------------------------------------------------------------------------------------------------------
def test_compound_forms(self):
url = self.apiPath + '/compounds/CHEMBL2107333/form.xml'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
forms = self.deserialize(resp, format='application/xml', tag='form')
self.assertEquals(len(forms), 1)
form = forms[0]
self.assertEquals(form['chemblId'], 'CHEMBL2107333')
url = self.apiPath + '/compounds/CHEMBL415863/form.xml'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
forms = self.deserialize(resp, format='application/xml', tag='form')
self.assertEquals(len(forms), 2)
form_1, form_2 = forms
self.assertEquals(form_1['chemblId'], 'CHEMBL1207563')
self.assertEquals(form_1['parent'], 'True')
self.assertEquals(form_2['parent'], 'False')
self.assertEquals(form_2['chemblId'], 'CHEMBL415863')
url = self.apiPath + '/compounds/CHEMBL278020/form'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
forms = self.deserialize(resp, format='application/json')['forms']
self.assertEquals(len(forms), 3)
form_1, form_2, form_3 = forms
self.assertEquals(form_1['chemblId'], 'CHEMBL211471')
self.assertEquals(form_2['chemblId'], 'CHEMBL54126')
self.assertEquals(form_3['chemblId'], 'CHEMBL278020')
url = self.apiPath + '/compounds/CHEMBL1207563/form'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
forms = self.deserialize(resp, format='application/json')['forms']
self.assertEquals(len(forms), 2)
form_1, form_2 = forms
self.assertEquals(form_1['chemblId'], 'CHEMBL1207563')
self.assertTrue(form_1['parent'])
self.assertFalse(form_2['parent'])
self.assertEquals(form_2['chemblId'], 'CHEMBL415863')
url = self.apiPath + '/compounds/CHEMBL1078826/form'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
forms = self.deserialize(resp, format='application/json')['forms']
self.assertTrue('CHEMBL1236196' in map(lambda x: x['chemblId'], forms))
for form in forms:
if form['chemblId'] == 'CHEMBL1236196':
self.assertTrue(form['parent'])
else:
self.assertFalse(form['parent'])
self.assertEquals(len(forms), 17)
url = self.apiPath + '/compounds/CHEMBL941/form'
resp = self.api_client.get(url, format='xml')
self.assertValidXMLResponse(resp)
forms = self.deserialize(resp, format='application/xml', tag='form')
self.assertEquals(len(forms), 2)
url = self.apiPath + '/compounds/CHEMBLX/form'
resp = self.api_client.get(url, format='json')
self.assertHttpBadRequest(resp)
url = self.apiPath + '/compounds/CHEMBL10000000000/form'
resp = self.api_client.get(url, format='json')
self.assertValidJSONResponse(resp, url)
forms = self.deserialize(resp, format='application/json')['forms']
self.assertEquals(len(forms), 0)
#-----------------------------------------------------------------------------------------------------------------------
def setUp(self):
super(EntryResourceTest, self).setUp()
self.serializer = ChEMBLApiSerializer()
self.api_client = TestApiClient(self.serializer)
self.apiPath = "/chembl_webservices/" + api.api_name
